Cellular Fractionation
Lamond Lab Protocol 2007
More detailed protocol can be found here: http://www.lamondlab.com/f7nucleolarprotocol.htm
This protocol has been adapted to fractionate a variety of different cell types into
cytoplasm, nucleoplasm and nucleoli. It uses a hypotonic buffer to swell the cells
prior to dounce homogenization to break them open. A series of centrifugations over
sucrose cushions follows, and nucleoli are released from purified nuclei by sonication.
The solutions that you need are listed below.
We also include a simplified version of the protocol, which can be used to fractionate
cells into cytoplasm and nuclei. This results in nuclei that are more pure than simply
stopping the full protocol after the second step. If you are only fractionating into
cytoplasm and nuclei, you will not need the S2 solution.
Solutions:
Buffer A (10 ml)
Hypotonic buffer that causes the cells to swell so that they can be efficiently broken open by dounce
homogenizing.
Stock
1 M HEPES, pH 7.9
1 M MgCl2
2.5 M KCl
1 M DTT
dH2O
Protease inhibitors
Volume (ml)
0.1
0.015
0.04
0.005
Up to 10 ml
1 Mini EDTA-free
COMPLETE tablet
mM (final)
10
1.5
10
0.5
S1 (0.25 M Sucrose, 10 mM MgCl2) 20 ml
Sucrose buffer used to fractionate nuclei.
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
1.96
0.2
Up to 20 ml
1 EDTA-free COMPLETE
tablet
mM (final)
0.25
10
S2 (0.35 M Sucrose, 0.5 mM MgCl2) 40 ml
Sucrose buffer used to sonicate nuclei and release nucleoli. The Mg level is critical, so remember to
always use EDTA-free protease inhibitor tablets!.
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
5.5
0.02
Up to 40 ml
2 EDTA-free COMPLETE
tablets
mM (final)
0.35
0.5
S3 (0.88 M Sucrose, 0.5 mM MgCl2) 20 ml
Sucrose buffer used to fractionate nucleoli.
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
6.9
0.01
Up to 20 ml
1 EDTA-free COMPLETE
tablet
mM (final)
0.88
0.5
RIPA Buffer (10 ml)
Detergent buffer used to solubilize proteins, either in whole cells or in purified cytoplasmic,
nucleoplasmic or nucleolar fractions.
Stock
1M Tris, pH 7.5
5 M NaCl
10% NP-40
10% Deoxycholate
Protease inhibitors
Volume (ml)
0.5
0.3
1
0.5
1 Mini EDTA-free
COMPLETE tablet
mM (final)
50
150
1%
0.5%
Starting Material:
We normally use between 5 and 15 x 14 cm dishes of confluent cells for this
fractionation.
Fractionation:
 Trypsinize cells, pellet at 1000 rpm for 4 min, wash with PBS and pellet again
at 1000 rpm for 4 min. Resuspend in 5 ml of ice-cold Buffer A and keep on
ice for 5 min. Break open cells to release nuclei using a pre-chilled 7 ml
Dounce homogenizer ( (10 strokes with a tight pestle).
 Centrifuge Dounced cells at 228 g (1000 rpm, Beckman GS-6, GH-3.8 rotor)
for 5 min at 4C to pellet nuclei and other fragments. The supernatant can be
retained as the cytoplasmic fraction.
 Resuspend the nuclear pellet in 3 ml of S1 and layer over a 3 ml cushion of
S2. Centrifuge at 1430 g (2500 rpm, Beckman GS-6, GH-3.8 rotor) for 5 min
at 4C. This step results in a cleaner nuclear pellet.
 Resuspend the clean, pelleted nuclei in 3 ml of S2 and sonicate for 6 x 10 sec
(with 10 sec rest between each sonication) at full power in an ice bath to
prevent overheating of the sample. Check the sonicate using phase contrast
microscopy to ensure that no intact nuclei remain, and that the nucleoli are
readily observable as dense, refractile bodies. If you still see intact nuclei,
continue to sonicate (adding 2 x 10 sec steps and checking again).
 Layer the sonicated sample over 3 ml of S3 and centrifuge at 2800 g (3500
rpm, Beckman GS-6, GH-3.8 rotor) for 10 min at 4C. The pellet contains the
nucleoli and the supernatant can be retained as the nucleoplasmic fraction.
 Wash the nucleoli by resuspending in 0.5 ml of S2 and centrifuge at 2800 g
(3500 rpm, Beckman GS-6, GH-3.8 rotor) for 5 min at 4C. They can be stored
in any volume of this buffer at -80C by snap-freezing them in liquid nitrogen.
Before using them they can be spun out of the buffer again with the same spin.
Fractionation of only cytoplasm and nuclei:
 Trypsinize cells, pellet at 1000 rpm for 4 min, wash with PBS and pelleet
again at 1000 rpm for 4 min. Resuspend in 5 ml of ice-cold Buffer A and
keep on ice for 5 min. Break open cells to release nuclei using a pre-chilled
Dounce homogenizer (20 strokes with a tight pestle).
 Centrifuge Dounced cells at 228 g (1000 rpm, Beckman GS-6, GH-3.8 rotor)
for 5 min at 4C to pellet nuclei and other fragments. The supernatant can be
retained as the cytoplasmic fraction.
 Resuspend the nuclear pellet in 3 ml of S1 and layer over a 3 ml cushion of
S3. Centrifuge at 2800 g (3500 rpm, Beckman GS-6, GH-3.8 rotor) for 10
min at 4C. This step results in a cleaner nuclear pellet.
Preparing lysates from cellular fractions:
We normally use RIPA buffer to prepare lysates from our cellular fractions. Pelleted
nuclei and nucleoli can be resuspended directly in 1X RIPA buffer, but cytoplasmic
and nucleoplasmic fractions will need to have 5X RIPA buffer added to them to bring
the final buffer as close to RIPA as possible. There will still be some small amount of
sucrose present in these lysates, but that can be minimized by increasing the final
lysate volume. Alternately, these fractions can be dialyzed into 1X RIPA buffer.
Full Fractionation (Cytoplasm, Nucleoplasm and Nucleoli)
Cytoplasmic Lysate:
The fractionation detailed above results in a 4 ml cytoplasmic fraction. We add 1 ml
of 5X RIPA buffer to this, mix well and then centrifuge at 2800 g (3500 rpm,
Beckman GS-6, GH-3.8 rotor) for 10 min at 4C to pellet any solids.
Nucleoplasmic Lysate:
The fractionation detailed above results in a 6 ml nucleoplasmic fraction. We add 2
ml of 5X RIPA buffer and 2 ml of dH2O to this, mix well and centrifuge at 2800 g
(3500 rpm, Beckman GS-6, GH-3.8 rotor) for 10 min at 4C to pellet any solids.
Nucleolar Lysate:
The fractionation detailed above results in a very small nucleolar pellet, which we
resuspend in 1 ml of 1X RIPA buffer and then sonicate 5 x 10 sec on ice to ensure
release of as many nucleolar proteins as possible.
Simple Fractionation (Cytoplasm and Nuclei)
Cytoplasmic Lysate:
The fractionation detailed above results in a 4 ml cytoplasmic fraction. We add 1 ml
of 5X RIPA buffer to this, mix well and then centrifuge at 2800 g (3500 rpm,
Beckman GS-6, GH-3.8 rotor) for 10 min at 4C to pellet any solids.
Nuclear Lysate:
The fractionation detailed above result in nuclear pellet of approximately 0.5 ml
volume. We add 5 ml of 1X RIPA buffer to this, mix well and then sonicate 5 x 10
sec on ice to ensure release of as many nuclear proteins as possible (and to shear
DNA). We then centrifuge the lysate at 2800 g (3500 rpm, Beckman GS-6, GH-3.8
rotor) for 10 min at 4C to pellet any solids.
Preparing larger volumes of buffers:
Buffer A (50 ml)
Stock
1 M HEPES, pH 7.9
Volume (ml)
0.5
1 M MgCl2
2.5 M KCl
1 M DTT
Protease inhibitors
0.075
0.2
0.025
1 EDTA-free COMPLETE tablet
S1 (0.25 M Sucrose, 10 mM MgCl2) 50 ml
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
4.9
0.5
Up to 50 ml
2 EDTA-free COMPLETE tablets
S2 (0.35 M Sucrose, 0.5 mM MgCl2) 50 ml
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
6.9
0.025
Up to 50 ml
2 EDTA-free COMPLETE tablets
S3 (0.88 M Sucrose, 0.5 mM MgCl2) 50 ml
Stock
2.5 M Sucrose
1 M MgCl2
dH2O
Protease inhibitors
Volume (ml)
17.3
0.025
Up to 50 ml
2 EDTA-free COMPLETE tablets
RIPA Buffer (50 ml)
Stock
1M Tris, pH 7.5
5 M NaCl
10% NP-40
10% Deoxycholate
Protease inhibitors
Volume (ml)
2.5
1.5
5
2.5
2 EDTA-free COMPLETE tablets